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Forum: Genomic Resequencing 05-03-2015, 01:11 PM
Replies: 0
Views: 1,586
Posted By dcard
Variant calling from paired/unpaired reads

I just happened upon a couple question threads in various places that warn against using both paired and non-paired reads for SNP calling.

https://www.biostars.org/p/140318/...
Forum: Bioinformatics 05-03-2015, 10:58 AM
Replies: 12
Views: 5,882
Posted By dcard
I just came across this error myself and figured...

I just came across this error myself and figured out a work-around. Steveped reported file names that should look familiar to anyone using Trimmomatic, as mine resembled those very closely. The error...
Forum: Bioinformatics 03-10-2015, 12:27 PM
Replies: 45
Views: 19,008
Posted By dcard
Optimal depth for read error correcting

Hi Brian and others,

I am wondering what depth you need and what depth is optimal (if the two differ) for proper read error correcting using BBMap or any other error correcting program. The Quake...
Forum: Bioinformatics 12-10-2014, 07:34 PM
Replies: 1
Views: 1,444
Posted By dcard
Assembling RADseq reads - Clustering vs. de novo assembly

Being interested in non-model vertebrates, myself and colleagues typically work with organisms without a closely-related reference genome. A common way of understanding species relationships and...
Forum: Bioinformatics 12-10-2014, 06:28 PM
Replies: 8
Views: 4,904
Posted By dcard
I just stumbled across this thread and thought...

I just stumbled across this thread and thought I'd contribute a bit and maybe help, if it is still needed. I haven't played a lot with dDocent, but I really like what it does in principle. The...
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